HHsearch alignment for GI: 254780611 and conserved domain: TIGR03001

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=98.37  E-value=3.8e-06  Score=60.59  Aligned_cols=82  Identities=21%  Similarity=0.414  Sum_probs=68.8

Q ss_conf             705655666666677799999962199999999999827888889899999977899999999----9999999999999
Q Consensus       210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI----~~~AL~kLR~~l~  285 (302)
T Consensus       142 DpEl~llr~~~r~~f~~Al~~Al~~L~~rER~LLRLHfv~~--Ls~~r~g~my~~~~STvsR~~~~ARe~lle~Tr~~La  219 (249)
T ss_conf             17899999999999999999987328986876555688203--3299998774577507899999999999999999999

Q ss_pred             HHHCCCCC
Q ss_conf             74012246
Q gi|254780611|r  286 KQVELSSS  293 (302)
Q Consensus       286 ~~~~~~~~  293 (302)
T Consensus       220 ~RL~L~~~  227 (249)
T TIGR03001       220 ERLKLSSR  227 (249)
T ss_pred             HHHCCCCH
T ss_conf             97488805